Ecosyste.ms: Issues
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GitHub / martinjzhang/scDRS issues and pull requests
#104 - Sig. cell type-disease associations and Sig. individual cells
Issue -
State: closed - Opened by hopehan12 17 days ago
- 3 comments
#103 - About the H5AD input - raw counts or normalized+transformed?
Issue -
State: closed - Opened by hopehan12 21 days ago
- 2 comments
#102 - Why are some of the CORR columns in the <trait>.scdrs_gene file negative, and the largest RANK level is the smallest negative number, can this represent the gene most associated with disease and cell type?
Issue -
State: closed - Opened by MoWeiLanChen 23 days ago
- 1 comment
#101 - scdrs perform-downstream: fail to load scDRS full score gz file
Issue -
State: closed - Opened by hopehan12 about 1 month ago
- 2 comments
#100 - Questions about reproducing results
Issue -
State: closed - Opened by HelloWorldLTY about 1 month ago
- 10 comments
#99 - The relationship between cell type association and heterogeneity
Issue -
State: open - Opened by AI-10 about 2 months ago
#98 - Questions about example dataset usage
Issue -
State: closed - Opened by HelloWorldLTY about 2 months ago
- 2 comments
#97 - Issue with plot using scdrs.util.plot_group_stats
Issue -
State: closed - Opened by NaomiHuntley about 2 months ago
- 2 comments
#96 - Update index.rst to fix a bug in the installation process
Pull Request -
State: closed - Opened by HelloWorldLTY about 2 months ago
- 2 comments
#95 - Questions about matched gene sets
Issue -
State: closed - Opened by HelloWorldLTY about 2 months ago
- 2 comments
#94 - Correcting cell-level p-values for multiple comparisons?
Issue -
State: open - Opened by schroeme about 2 months ago
- 3 comments
#93 - fail to get the "1000 top associated genes" based on MAGMA
Issue -
State: closed - Opened by yihancc 2 months ago
- 2 comments
#92 - use scdrs in a tissue seemlingly unrelated with the disease
Issue -
State: closed - Opened by Davidseye 3 months ago
- 7 comments
#91 - tcell.facs.annot.h5ad without GENE name
Issue -
State: closed - Opened by Davidseye 3 months ago
- 2 comments
#90 - Preprocessing: killed running scdrs compute-score
Issue -
State: closed - Opened by schroeme 4 months ago
- 4 comments
#89 - Converting GWAS catalog .tsv file to gene set
Issue -
State: closed - Opened by kayihui 4 months ago
- 3 comments
#88 - ValueError: too many values to unpack (expected 2)
Issue -
State: closed - Opened by kayihui 4 months ago
- 8 comments
#87 - Using geneset from SMR result
Issue -
State: closed - Opened by Misaka-15134 4 months ago
- 1 comment
#86 - Interpreting scDRS score when comparing cell-type subclusters
Issue -
State: open - Opened by HyeonbinJoHCho 4 months ago
- 1 comment
#85 - Issue83
Pull Request -
State: closed - Opened by martinjzhang 5 months ago
#84 - The 'n_fdr_0.2' number of all group is 0
Issue -
State: closed - Opened by Y-Isaac 5 months ago
- 7 comments
#83 - AssertionError when running quick test after installation
Issue -
State: closed - Opened by hoholee 6 months ago
- 7 comments
#82 - trait=z_score: skipped due to small size (n_gene=5, sys_time=116.1s)
Issue -
State: closed - Opened by Lualululu 7 months ago
- 1 comment
#81 - TypeError: plot_group_stats() got an unexpected keyword argument 'plot_kws'
Issue -
State: closed - Opened by Huiflorazhan 8 months ago
- 16 comments
#80 - Is it reasonable to use human' geneset on mouse scRNAseq data?
Issue -
State: closed - Opened by zehualilab 8 months ago
- 2 comments
#79 - About compute-score
Issue -
State: closed - Opened by evenDDDDD 8 months ago
#78 - TypeError: '<' not supported between instances of 'str' and 'float'
Issue -
State: closed - Opened by zehualilab 9 months ago
- 3 comments
#77 - Subsetting cells for downstream analysis.
Issue -
State: closed - Opened by jeji0209 10 months ago
- 1 comment
#76 - fixed the bug in scdrs/util.py
Pull Request -
State: closed - Opened by yyoshiaki 10 months ago
- 2 comments
#75 - add option for specifying FDR threshold in plot_group_stats
Pull Request -
State: closed - Opened by KangchengHou 11 months ago
- 3 comments
#74 - The graphs from a single result and multiple results are inconsistent
Issue -
State: closed - Opened by QianChwnLyn 11 months ago
- 13 comments
#73 - custom gene set ?
Issue -
State: closed - Opened by zhangpicb 11 months ago
- 2 comments
#72 - compute-score is not reading .gs file properly
Issue -
State: closed - Opened by juliaapolonio 11 months ago
- 2 comments
#71 - Gene weights or without gene weights
Issue -
State: closed - Opened by QianChwnLyn 12 months ago
- 3 comments
#70 - Update dependencies of scDRS
Issue -
State: open - Opened by martinjzhang about 1 year ago
Labels: bug
#69 - gene weights for the control genes
Issue -
State: closed - Opened by aandreas13 about 1 year ago
- 5 comments
#68 - Issues Plotting UMAP from quick start tutorial
Issue -
State: closed - Opened by NaomiHuntley about 1 year ago
- 1 comment
#67 - error metaclass conflict
Issue -
State: closed - Opened by jhong26 over 1 year ago
- 1 comment
#66 - turning off fdr correction
Issue -
State: closed - Opened by milospjanic over 1 year ago
- 1 comment
#65 - plot_group_stats() got an unexpected keyword argument 'plot_kws'
Issue -
State: closed - Opened by milospjanic over 1 year ago
- 15 comments
#64 - perform-downstream outputs zero significant cells
Issue -
State: closed - Opened by gwentea over 1 year ago
- 1 comment
#63 - scRNA data input
Issue -
State: closed - Opened by frucelee over 1 year ago
- 6 comments
#62 - Error in scdrs perform-downstream --group-analysis
Issue -
State: closed - Opened by jiawei-zhong over 1 year ago
- 4 comments
#61 - munge-gs input format
Issue -
State: closed - Opened by DonaldSandoz2000 over 1 year ago
- 2 comments
#60 - Remove NA values in corr anlaysis
Issue -
State: open - Opened by martinjzhang over 1 year ago
#59 - Convert Seurat object to h5ad file
Issue -
State: open - Opened by uqzqiao over 1 year ago
- 19 comments
#58 - update doc: clatify raw p-val; procedure to increase MC samples in gr…
Pull Request -
State: closed - Opened by martinjzhang over 1 year ago
#57 - scdrs compute-score output
Issue -
State: closed - Opened by NaomiHuntley over 1 year ago
- 4 comments
#56 - Please help with scDRS for the plant Arabidopsis thaliana
Issue -
State: closed - Opened by bitcometz over 1 year ago
- 15 comments
#55 - Update compute_magma_gs.md
Pull Request -
State: closed - Opened by KangchengHou over 1 year ago
#54 - "skipped due to small size" error
Issue -
State: closed - Opened by NaomiHuntley over 1 year ago
- 9 comments
#53 - Issue52
Pull Request -
State: closed - Opened by martinjzhang over 1 year ago
#52 - Error when adata.obs_names can be interpreted as integers
Issue -
State: closed - Opened by daxxio over 1 year ago
- 2 comments
#51 - Considerations for single cell splicing data
Issue -
State: open - Opened by dbogdano over 1 year ago
- 2 comments
#50 - tutorial-Quick start ——full_score.gz
Issue -
State: closed - Opened by zhouxilala almost 2 years ago
- 1 comment
#49 - GWAS traits and a control traits
Issue -
State: closed - Opened by Li-mengjie almost 2 years ago
- 12 comments
#48 - Adjusting for donor effects
Issue -
State: closed - Opened by Ararder almost 2 years ago
- 1 comment
#47 - Multiple testing correction on downstream analysis
Issue -
State: closed - Opened by aandreas13 almost 2 years ago
- 2 comments
#46 - compute-score can not complete
Issue -
State: closed - Opened by Dan-121 almost 2 years ago
- 7 comments
#45 - scdrs CLI not working?
Issue -
State: closed - Opened by Dzhan4 almost 2 years ago
- 3 comments
#44 - Seurat to h5ad
Issue -
State: closed - Opened by Dzhan4 almost 2 years ago
- 7 comments
#43 - Cell-type disease association vs proportion of significant cells
Issue -
State: closed - Opened by DanielYuhangLi almost 2 years ago
- 2 comments
#42 - concerning beta or OR when choosing putative disease genes
Issue -
State: open - Opened by parkjooyoung99 almost 2 years ago
- 1 comment
#41 - check input in munge-gs
Pull Request -
State: closed - Opened by KangchengHou almost 2 years ago
#40 - munge-gs type error
Issue -
State: closed - Opened by parkjooyoung99 almost 2 years ago
- 2 comments
#39 - Negative weights in munge-gs
Issue -
State: open - Opened by martinjzhang almost 2 years ago
#38 - Issues with generating gs files
Issue -
State: closed - Opened by Li-mengjie almost 2 years ago
- 1 comment
#37 - Problem with munging
Issue -
State: closed - Opened by HJ234 about 2 years ago
- 6 comments
#36 - Adding arguments of min_cells and min_genes to CLI for data filtering
Issue -
State: closed - Opened by martinjzhang about 2 years ago
- 1 comment
Labels: enhancement
#35 - Issue32
Pull Request -
State: closed - Opened by martinjzhang about 2 years ago
- 1 comment
#34 - Print cell type info
Issue -
State: closed - Opened by martinjzhang about 2 years ago
Labels: enhancement
#33 - Segmentation fault when Running scDRS
Issue -
State: closed - Opened by angelussong about 2 years ago
- 4 comments
#32 - Data sparsity is a critical problem for the inference stability (ex. 10x data)
Issue -
State: closed - Opened by yyoshiaki about 2 years ago
- 11 comments
Labels: enhancement, good first issue, question
#31 - scDRS CLI scdrs munge-gs
Issue -
State: closed - Opened by Alina-Song about 2 years ago
- 1 comment
#30 - Broader control gene sets
Issue -
State: open - Opened by kitscorp about 2 years ago
- 1 comment
Labels: enhancement, question
#29 - Problems with input data
Issue -
State: closed - Opened by Mia1037 about 2 years ago
- 6 comments
Labels: documentation, question
#28 - doc v1.0.2
Pull Request -
State: closed - Opened by martinjzhang about 2 years ago
#27 - Drop duplicates for pval_file and zsc_file
Issue -
State: closed - Opened by martinjzhang about 2 years ago
Labels: enhancement
#26 - Check inputs
Issue -
State: closed - Opened by martinjzhang about 2 years ago
Labels: enhancement
#25 - Loess error in compute-score after subsampling
Issue -
State: closed - Opened by twoneu about 2 years ago
- 5 comments
#24 - KeyError: at plot_group_stats step
Issue -
State: closed - Opened by twoneu about 2 years ago
- 12 comments
Labels: bug
#23 - scDRS breaks if using all scRNA-seq genes as disease genes
Issue -
State: open - Opened by martinjzhang about 2 years ago
Labels: enhancement
#22 - cope with categorical covariates
Pull Request -
State: closed - Opened by KangchengHou about 2 years ago
#21 - Accept categorical covariates
Issue -
State: closed - Opened by martinjzhang about 2 years ago
#20 - Ordinal covariates
Issue -
State: closed - Opened by rbutleriii about 2 years ago
- 2 comments
#19 - Cleaning/prepping GWAS statistics
Issue -
State: closed - Opened by rbutleriii about 2 years ago
- 2 comments
#18 - Tutorial for preparing files
Issue -
State: closed - Opened by martinjzhang over 2 years ago
#17 - MC-z and MC-z-based p-value
Issue -
State: closed - Opened by martinjzhang over 2 years ago
- 2 comments
#16 - Correct ctp
Pull Request -
State: closed - Opened by martinjzhang over 2 years ago
#15 - Test cli
Pull Request -
State: closed - Opened by martinjzhang almost 3 years ago
- 2 comments
#14 - Continuous weight experiment
Pull Request -
State: closed - Opened by KangchengHou almost 3 years ago
#13 - Test cli
Pull Request -
State: closed - Opened by martinjzhang almost 3 years ago
#12 - Change munge-gs; unit tests for munge-gs, load_gs, load_homolog_mapping
Pull Request -
State: closed - Opened by martinjzhang almost 3 years ago
#11 - Unit test
Pull Request -
State: closed - Opened by martinjzhang almost 3 years ago
#10 - Unit test
Pull Request -
State: closed - Opened by martinjzhang almost 3 years ago
#9 - Issue with test run
Issue -
State: closed - Opened by tkamath1 almost 3 years ago
- 5 comments
#8 - Updated cli
Pull Request -
State: closed - Opened by KangchengHou almost 3 years ago
#7 - Merge sparse to dense
Pull Request -
State: closed - Opened by martinjzhang almost 3 years ago
#6 - Gene weights
Pull Request -
State: closed - Opened by KangchengHou almost 3 years ago
#5 - sparse_mz
Pull Request -
State: closed - Opened by martinjzhang almost 3 years ago